Characteristics of mRNAs enriched or depleted for Upf1-associated ribosomes. (A) Results of differential expression analyses by DESeq2 between mRNA abundance in IP versus Total ribosome profiling libraries of each strain and CHX treatment. False discovery rate (FDR) with a threshold of 0.05 was used to determine significant differential expression. mRNAs with adjusted P-value <0.05 and positive log2(IP/Total) were considered enriched in IP libraries (orange), whereas those with adjusted P-value <0.05 and negative log2(IP/Total) were considered depleted in IP libraries (purple); otherwise, their abundance did not differ (“unchanged”) between IP and Total (gray). (B–D) Comparative analyses of ribosome occupancy (B), coding sequence length (C), and codon optimality score (D) between mRNA groups identified in A. Two-tailed Wilcoxon's rank sum test with FDR method for multiple testing correction was used to compare each pair of mRNA groups. Symbols for levels of significance are ns: P > 0.05, (*) P < 0.05, (**) P < 0.01, (***) P < 0.001, (****) P < 0.0001. Number of mRNAs in each group is provided. Outlier mRNAs (those beyond the whiskers of box plots) were included in the analyses but omitted from plotting.
